New Japanese database reveals how gut microbes and diet connect

New Japanese database reveals how gut microbes and diet connect

With the launch of the NIBN Japan Microbiome Database, scientists gain an unprecedented window into how lifestyle and diet shape our microbiome and influence long-term health.

In a recently published study inScientific reportsResearchers introduced the NIBN Japan Microbiome Database (NIBN JMD), a large, publicly available database of diverse, healthy human microbiome profiles (containing more than 2,000 microbiome samples) with up to 1,000 metadata points per sample, as well as longitudinal studies.

The database aims to facilitate and advance future microbiome association studies and medical research by providing researchers with a comprehensive baseline data set against which to compare gut microbiome impacts and causal associations, paving the way for microbiome-associated chronic disease and lifestyle interventions. This article describes the NIBN JMD database, its features and potential applications.

background

The samples came from nine different locations in six Japanese prefectures, including urban centers such as Tokyo and Osaka as well as rural areas such as Minamiuonuma, improving regional diversity.

A growing body of research highlights the importance of the human gut microbiome in shaping host health and disease. Studies have established a strong bidirectional relationship between gut microbiome characteristics (composition and relative densities of gut flora) and clinical outcomes, including obesity, infections, inflammation, and even cancers.

While significant advances in next-generation sequencing technologies (including genomics, proteomics, and transcriptomics) have provided scientists with unprecedented amounts of microbiome data, existing datasets suffer from the common threads of inadequate metadata and contextual annotation. In addition, traditional databases provide summary statistics calculated by aggregated data from multiple studies, but they do not take into account the methodological differences between studies.

These limitations hinder generalizable, large-scale investigations of interactions with microbiome health, thereby hindering the discovery and deployment of interventions targeting a broad range of diets, lifestyles, and diseases. This requires the development of a standardized human microbiome database that includes both diverse sequencing data and thorough metadata annotation, which would facilitate harnessing the full potential of the gut microbiome in mitigating human disease and promoting global well-being.

What is Nibn JMD?

The researchers used a custom pipeline called “SNAQ” for 16S data analysis, which included specific quality thresholds (BBDUK trimming) and the Silva database version 138 for taxonomy.

The National Institutes of Biomedical Innovation, Health and Nutrition (NIBN, formerly Nibiohn) is a Japanese collaborative research effort between the National Institute of Biomedical Innovation (NIBIO) and the National Institute of Health and Nutrition (NIHN). Founded in 2005, the organization aims to advance biomedical innovation, nutrition and pharmaceutical production for the Japanese population.

NIBN recognized gaps in current human microbiome databases and addressed this recruitment of stool samples and extensive metadata from both its own extensive research network and multiple collaborators to generate one of the largest human microbiome datasets in existence. This novel database, named “NIBN Japan Microbiome Database (NIBN JMD),” this novel database, which is publicly available with some limitations, aims to unleash the true clinical potential of the human gut microbiome through unprecedented metadata annotation and a self-assembly design.

The database currently includes 2,273 microbiome samples from 2,068 subjects, each connected to up to 1,000 metadata points, covering participant demographics, diets, lifestyles, physical activity and medical history. While all samples have basic metadata, the level of detail depends on the specific cohort. The database also contains collaborator-derived longitudinal samples, enabling analyzes of temporal microbiome dynamics. Notably, all data processing adhered to standardized protocols to maintain consistency and reliability across a variety of samples.

How was Nibn JMD developed and what are its key features?

Age data were carefully divided into areas of anonymity to ensure at least five participants per group, classified separately by gender and cohort.

The researchers used a snakemake pipeline for Qiime2 called “SNAQ” to process 16S rRNA sequencing data, while separate internal pipelines were used for shotgun metagenomic data. The latter pipelines include provisions for automating NCBI-compliant taxonomic tasks (Kraken 2, Bracken and Metaphlan), functional profiles (FMAP) and metadata annotation. The paper notes that during shotgun sequencing, full analysis results will be available in a future version of the database.

The NIBN JMD is based on a custom implementation of the Manta platform, which provided researchers with a range of built-in multifactorial analysis tools capable of visualizing microbiome-health associations and exploring correlations within the data. The researchers also developed an internal script to automate importing and processing data from new and future samples.

Most importantly, NIBN JMD represents a rich, well-structured data set, architecturally focused on user-friendly access and capable of integrating with most gold standard analytical tools. The public interface supports open science and hopes to revolutionize future collaborative microbiome studies. While basic data is openly available, access to more comprehensive metadata requires a collaborative agreement and institutional review board (IRB) approval to ensure ethical handling of data.

Conclusions

NIBN JMD represents a significant advance in the microbiome research infrastructure, providing scientists with a richly annotated, publicly available resource – one of the largest and most comprehensive of its kind. It complements other global resources with high consistency and interactive analysis tools. This database has the potential to accelerate discoveries in microbiome science, inform personalized health strategies, and accelerate the development of interventions that utilize the microbiome.

It has already been used in studies establishing associations between gut microbiota and factors such as dietary patterns (including barley and vitamin B1 intake), bowel habits and metabolic diseases such as obesity and type 2 diabetes. While its current limitation for Japanese participants limits its global generalizability, it shows the first step toward a healthier tomorrow.

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